I have an S2R 1000 with Full Arrow Ti and ran it with stock ECU & airbox.
I pulled the baffles and the bike ran like "poo" - very rough, surging, stalling, popping, etc. So I put the baffles back in. In short, you probably would hurt the engine if you put on 1000's of kilometers without the baffles because it is (obviously) way too lean - but why would you do that when it runs so poorly? But there is no harm in trying it out (if even to see how loud it is >

), maybe the S4R will be different.
I have since upgraded to the DP ECU. Baffles or not, the bike now runs as it should have from the factory (if not for the emission laws)...